Fiddling the Football Stadia Improvement Fund is one of sport's nastier strains of corruption. The service, providing grants for clubs to make their grounds decent, was hugely boosted with public money only after 96 Liverpool supporters lost their lives at Hillsborough in 1989. Club directors who cheat such a fund, set up to help them, deserve all the sanctions and contempt the game can muster, you might think.

So when last month Macclesfield Town were found guilty by a Football Association "disciplinary commission" on three counts of improper conduct relating to a grant on their new £1.5m stand in 2001 and ordered to pay fines and compensation of around £300,000 by the end of January, you might assume justice had been served. In the Silkmen's case, however, one of the League's smallest clubs, it does not quite feel that way. The difficulty is that it is impossible to judge the merit of the decision because the FA's disciplinary procedures are cloaked in secrecy.

Certainly at Macclesfield, the affair does not involve heinous offences like inflated invoices, dodgy tenders or the lining of individuals' pockets.

Since the alleged offences the ownership of the club and all the directors have changed. The former chairman Eddie Furlong has always denied any malpractice. The current chairman, Rob Bickerton, is supportive of his predecessors, although he says they made "an error". He measures his words but clearly believes the club have been harshly and unjustly treated.

Macclesfield did admit two charges of improper conduct and were fined £10,000 for each. One was that the club received grant money from the FSIF before paying the contractor, Alfred McAlpine, for doing the work; the FA's rules require clubs to pay builders first, then put a claim in, to prevent grant money being used for other things. Macclesfield also admitted receiving cash, around £50,000, then not paying McAlpine for some of its work.

The third guilty finding was the heaviest, devastating fans of the Cheshire club, then sending them into a frenzy of fundraising. The new stand, comprising 1,550 seats along the Easter Road side of the intimate Moss Rose ground, cost, Bickerton says, around £1.5m. When McAlpine finished it, the company paid Macclesfield approximately £245,000 in sponsorship, against invoices raised by the club. For that it was called the Alfred McAlpine Stand and will be for 10 years.

The FA's disciplinary commission decided this was a breach of the rules. It was not "genuine sponsorship" but was a discount of £245,000. FSIF grants pay up to 80% of any ground improvement and clubs have to find the rest. According to the FA's decision, the grant to Macclesfield was excessive because the true cost on which the club claimed had been discounted, so the club were ordered to repay 80% of the £245,000 - around £195,000 - and fined £40,000 for this improper conduct. They were also given a £2,000 fine for a lesser charge relating to the way their accounts recorded transactions between the club and one of the directors' companies.

Bickerton says Macclesfield continue to believe they had a genuine sponsorship agreement with McAlpine, a blue-chip construction company, covered by invoices and correspondence.

Altogether, with their own and the FA's costs to pay, Macclesfield Town have to find £300,000 by the end of this month, a figure Bickerton describes as "staggering". Macc were already struggling financially, with home gates mostly dipping under 2,000 this season as Brian Horton's team has struggled, and had already announced several redundancies including the assistant manager John Askey, a former player who made 700 appearances for the club.

Since 2003 there have been new owners, Amar and Bashar Alkadhi, two Iraqi-born businessmen described as genuine fans by Bickerton, who support the club with interest-free loans but are not prepared to stump up £300,000 for alleged breaches of rules before their time.

The FA's decision, Bickerton said, was devastating. "I felt it was the death of Macc Town and I might as well go to the ground the following morning and post the keys through the letter box."

Instead he let himself in at 6am and watched as emails of support started dropping in. At 8 o'clock fans began ringing, promising money and time. The Save Our Silkmen campaign was born, with initiatives ranging from sponsoring a seat in the McAlpine Stand for £50 to asking the Football League to move the match against Carlisle from Saturday January 28 to Sunday 29, to designate it a "Fans United" day and ask fans from all over to come to the Moss Rose.

Bickerton said: "This crisis has shown how much these people care about their football club; they support it with huge passion and loyalty. We're determined to raise this money and emerge stronger than we were before."

Football's recent past is decorated with awesome rescues by supporters of clubs on the edge of ruin but at Macclesfield there is anger, too. Many fans are urging Bickerton to challenge the FA, not only its findings but the whole disciplinary process.

The FA may well be justified in concluding the deal was a breach of the rule that a club must contribute 20% and that sponsorship was not paid separately from the full building cost of the stand. However, we cannot know how it reached the decision because it makes no details public, saying only on its website: "The Commission found this charge to be proven."

Nor are we even allowed to know who sat in judgment on "The Commission" because the FA does not make that public either. Bickerton said the first thing the commission's chairman said when he arrived at the hearing was: "Everything that happens here is confidential." He has obeyed that command.

Many fans, however, feel that their club's existence has been placed into severe jeopardy by a governing body acting as prosecutor, judge and jury, secretively, with no accountability.

The FA has told Macclesfield it will deliver written reasons shortly and the club may then consider whether to appeal or mount any other legal challenge. These arcane disciplinary procedures are being reviewed by the FA; within the organisation many accept the procedures need to become more independent and transparent.

In the meantime all efforts at the Moss Rose are on raising money: fans of other clubs have already bought pixels on www.mtfc.info a sponsored wheelchair push is planned, along with all manner of rallying round. Like other clubs before them, Macclesfield will survive.

The original Macclesfield Football Club began playing in 1874 and went bust twice, in 1897 and the first world war.

The club's journey to the Conference title and promotion to the Football League in 1997 took in Northern Premier League championships in 1969 and 1970 and Conference triumphs in 1995 and 1997, but their history is studded with crises, recording: "severe financial problems" in 1936; "a club ravaged by financial crisis" in 1975-76; and in 1996-97, the most successful season in the club's history, problems off the field which "threatened the future of the club".

The Moss Rose ground's record attendance is 9,008 for the Cheshire Senior Cup second-round tie against Winsford United in 1967. Macc Town have won the trophy 20 times.

Capacity at the Moss Rose is now 6,235.

With gates averaging 2,165 this season, Macclesfield are one of the Football League's smallest clubs.

The club has been ordered to pay fines of £62,000 for four breaches of FA rules, repay £195,000 to the Football Stadia Improvement Fund, plus the costs of the disciplinary hearing, which amounts to £300,000 to be repaid by the end of this month.